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Eukaryotic rRNA Evolution: Early Diverging Eukaryotes (dm)

Pelobionts are flagellated protists that inhabit micro-oxic and anoxic environments. They represent one group of eukaryotes that has been identified as a potentially deep-branching eukaryotic lineage on the basis of ultrastructure and certain molecular phylogenies. Because they lack stacked dictyosomes, mitochondria, and outer dynein arms in their flagellar apparatus, pelobionts might represent early diverging eukaryotic lineages.

Molecular analyses of DNA-dependent RNA polymerase II suggest the pelobiont Mastigamoeba invertens diverged early. Analyses of SSU (small subunit) ribosomal RNAs, in contrast, position pelobionts near the eukaryotic “crown groups”, but not as a monophyletic group. We sequenced SSU rRNA genes from four additional pelobiont taxa (including two new isolates). This work confirmed the sequence for M. invertens by in situ hybridization, compared the ultrastructural features of these taxa, and subjected these new pelobiont sequences to a rigorous phylogenetic analysis in the context of a larger alignment of eukaryotes, including known sequences from other pelobionts.

Results show that despite the absence of typical eukaryotic organelles, e.g., mitochondria, dictyosomes, chloroplasts, coated vesicles, and peroxisomes, pelobionts are not basal to other eukaryotes in our molecular analyses nor are they specifically related to a previously described pelobiont-like organism, Mastigamoeba invertens. This result calls into question the taxonomic assignment of this organism and the phylogenetic methodologies that placed it as a deep-diverging eukaryotic lineage. Independent of the evolutionary models tested, sequence alignments employed, and taxon sampling, the pelobionts (exclusive of M. invertens) form a monophyletic group together with Endolimax nana in maximum likelihood, distance and parsimony inferences. Many analyses suggest the pelobionts share common ancestry with the Entamoebidae, with E. nana sharing an unique common evolutionary history with Mastigamoeba simplex. Pelobionts do not represent one of the earliest branching lineages as suggested by RNA polymerase II and ultrastructure.